The Evolving Role of Molecular Markers in the Diagnosis and Management of Diffuse Glioma

Transforming brain cancer biomarker research with patinformatics and SWOT analysis

Brain cancer heterogeneity imposes significant challenges in diagnosis, causing high mortality. The lack of timely diagnosis intensifies these challenges, underscoring the need for improved diagnostics. Recent advancements in biomarker discovery have led to biomarker detection at ultra-low concentrations via multiplexing with biosensors, offering a promising avenue for the timely detection of brain cancer. Serving as a comprehensive resource, this review highlights the crucial role of primary biomarkers in brain cancer diagnosis via integration of patinformatics and SWOT analysis, thereby facilitating timely diagnosis and informed decision making. Furthermore, we aim to outline recent advances in brain cancer prognostics and management strategies, ultimately improving patient outcomes.

Current research status of Raman spectroscopy in glioma detection

Glioma is the most common primary tumor of the nervous system. Conventional diagnostic methods for glioma often involve time-consuming or reliance on externally introduced materials. Consequently, there is an urgent need for rapid and reliable diagnostic techniques. Raman spectroscopy has emerged as a promising tool, offering rapid, accurate, and label-free analysis with high sensitivity and specificity in biomedical applications. In this review, the fundamental principles of Raman spectroscopy have been introduced, and then the progress of applying Raman spectroscopy in biomedical studies has been summarized, including the identification and typing of glioma. The challenges encountered in the clinical application of Raman spectroscopy for glioma have been discussed, and the prospects have also been envisioned.

Prognostic significance of oligodendrocyte transcription factor 2 expression in glioma patients: A systematic review and meta-analysis

BACKGROUND

Gliomas are the most common primary central nervous system neoplasm. Despite recent advances in the diagnosis and treatment of gliomas, patient prognosis remains dismal. Therefore, it is imperative to identify novel diagnostic biomarkers and therapeutic targets of glioma to effectively improve treatment outcomes.

AIM

To investigate the association between oligodendrocyte transcription factor 2 (Olig2) expression and the outcomes of glioma patients.

METHODS

The PubMed, Embase, Cochrane Library, and China National Knowledge Infrastructure databases were searched for studies (published up to October 2023) that investigated the relationship between Olig2 expression and prognosis of glioma patients. The quality of the studies was assessed using the Newcastle Ottawa Scale. Data analyses were performed using Stata Version 12.0 software.

RESULTS

A total of 1205 glioma patients from six studies were included in the meta-analysis. High Olig2 expression was associated with better outcomes in glioma patients [hazard ratio (HR): 0.81; 95% (confidence interval) CI: 0.51-1.27; P = 0.000]. Furthermore, the results of subgroup meta-analysis showed that high expression of Olig2 was associated with poor overall survival in European patients (HR: 1.34; 95%CI: 0.79-2.27) and better prognosis in Asian patients (HR: 0.43; 95%CI: 0.22-0.84). The sensitivity analysis showed that no single study had a significant effect on pooled HR, and there was also no indication of publication bias according to the Egger's and Begger's P value test or funnel plot test.

CONCLUSION

High Olig2 expression may have a positive impact on the prognosis of glioma patients, and should be investigated further as a prognostic biomarker and therapeutic target for glioma.

Rapid detection of IDH mutations in gliomas by intraoperative mass spectrometry

The development and performance of two mass spectrometry (MS) workflows for the intraoperative diagnosis of isocitrate dehydrogenase (IDH) mutations in glioma is implemented by independent teams at Mayo Clinic, Jacksonville, and Huashan Hospital, Shanghai. The infiltrative nature of gliomas makes rapid diagnosis necessary to guide the extent of surgical resection of central nervous system (CNS) tumors. The combination of tissue biopsy and MS analysis used here satisfies this requirement. The key feature of both described methods is the use of tandem MS to measure the oncometabolite 2-hydroxyglutarate (2HG) relative to endogenous glutamate (Glu) to characterize the presence of mutant tumor. The experiments i) provide IDH mutation status for individual patients and ii) demonstrate a strong correlation of 2HG signals with tumor infiltration. The measured ratio of 2HG to Glu correlates with IDH-mutant (IDH-mut) glioma (P < 0.0001) in the tumor core data of both teams. Despite using different ionization methods and different mass spectrometers, comparable performance in determining IDH mutations from core tumor biopsies was achieved with sensitivities, specificities, and accuracies all at 100%. None of the 31 patients at Mayo Clinic or the 74 patients at Huashan Hospital were misclassified when analyzing tumor core biopsies. Robustness of the methodology was evaluated by postoperative re-examination of samples. Both teams noted the presence of high concentrations of 2HG at surgical margins, supporting future use of intraoperative MS to monitor for clean surgical margins. The power of MS diagnostics is shown in resolving contradictory clinical features, e.g., in distinguishing gliosis from IDH-mut glioma.

Promising outcome of patients with recurrent glioblastoma after Gamma Knife-based hypofractionated radiotherapy

BACKGROUND

The role of Gamma Knife radiosurgery (GKRS) in recurrent glioblastoma remains unclear. The purpose of this study is to evaluate the effects of GKRS in a group of patients with recurrent glioblastoma, focusing on survival and safety.

METHODS

Patients undergoing GKRS for recurrent glioblastoma between September 2014 and April 2019 were included in this study. Relevant clinical and radiosurgical data, including GKRS-related complications, were recorded and analyzed. Overall survival (OS), local progression free survival (LPFS) and prognostic factors for outcome were thoroughly evaluated.

RESULTS

Fifty-three patients were analyzed (24 female, 29 male). The median age was 50 years (range, 19-78 years). The median GKRS treatment volume was 35.01 cm3 (range, 2.38-115.57 cm3). Twenty patients (38%) were treated with single fraction GKRS, while 33 (62%) were treated with GKRS-based hypofractionated stereotactic radiotherapy (HSRT). The median prescription dose for single fraction GKRS, 3-fractions HSRT and 5-fractions HSRT were 16 Gy (range, 10-20 Gy), 27 Gy (range, 18-33 Gy) and 25 Gy (range, 25-30 Gy), respectively. The median LPFS and OS times were 8.1 months and 11.4 months after GKRS, respectively. HSRT and Bevacizumab were associated with improved LPFS, while HSRT alone was associated with longer OS.

CONCLUSION

Our findings suggested that HRST would likely improve LPFS and OS in definite settings; the addition of Bevacizumab to GKRS was associated with increased rates of local control. No major complications were reported. Further prospective studies are warranted to confirm our findings.

Glutamine metabolism-related genes predict prognosis and reshape tumor microenvironment immune characteristics in diffuse gliomas

Background

Diffuse gliomas possess a kind of malignant brain tumor with high mortality. Glutamine represents the most abundant and versatile amino acid in the body. Glutamine not only plays an important role in cell metabolism but also involves in cell survival and malignancies progression. Recent studies indicate that glutamine could also affect the metabolism of immune cells in the tumor microenvironment (TME).

Materials and methods

The transcriptome data and clinicopathological information of patients with glioma were acquired from TCGA, CGGA, and West China Hospital (WCH). The glutamine metabolism-related genes (GMRGs) were retrieved from the Molecular Signature Database. Consensus clustering analysis was used to discover expression patterns of GMRGs, and glutamine metabolism risk scores (GMRSs) were established to model tumor aggressiveness-related GMRG expression signature. ESTIMATE and CIBERSORTx were applied to depict the TME immune landscape. The tumor immunological phenotype analysis and TIDE were utilized for predicting the therapeutic response of immunotherapy.

Results

A total of 106 GMRGs were retrieved. Two distinct clusters were established by consensus clustering analysis, which showed a close association with the IDH mutational status of gliomas. In both IDH-mutant and IDH-wildtype gliomas, cluster 2 had significantly shorter overall survival compared with cluster 1, and the differentially expressed genes between the two clusters enriched in pathways related to malignant transformation as well as immunity. In silico TME analysis of the two IDH subtypes revealed not only significantly different immune cell infiltrations and immune phenotypes between the GMRG expression clusters but also different predicted responses to immunotherapy. After the screening, a total of 10 GMRGs were selected to build the GMRS. Survival analysis demonstrated the independent prognostic role of GMRS. Prognostic nomograms were established to predict 1-, 2-, and 3-year survival rates in the four cohorts.

Conclusion

Different subtypes of glutamine metabolism could affect the aggressiveness and TME immune features of diffuse glioma, despite their IDH mutational status. The expression signature of GMRGs could not only predict the outcome of patients with glioma but also be combined into an accurate prognostic nomogram.

Immune Characteristics and Prognosis Analysis of the Proteasome 20S Subunit Beta 9 in Lower-Grade Gliomas

Glioma is a common intracranial malignancy in adults and has a high mortality due to its poor prognosis and high recurrence rate. Dysregulation of protein degradation is one of the main promoting factors in glioma development. As an indispensable unit of the proteasome, Proteasome 20S Subunit Beta 9 (PSMB9) is one of the major enzymes in ubiquitin-dependent protein degradation in cells. In addition, proteasomes also participate in a series of cellular processing, like immune regulation, nerve signal transduction, material transport through channels, cell adhesion, and various signaling pathways. However, the relationship between the PSMB9 expression and the occurrence of lower-grade glioma (LGG) is still unknown. First, we collected the RNA-seq and clinical information about LGG clinical samples from The Cancer Genome Atlas (TCGA) cohort, Chinese Glioma Genome Atlas (CGGA; including CGGAseq1 and CGGAseq2) cohort, and Gene Expression Omnibus (GEO; GSE16011, GSE61374, and Rembrandt) cohort. Then, these data were used for differential analysis, survival analysis, enrichment analysis, clinical model construction, etc. In addition, we combine immune-related data for immune-related analysis, including immune infiltration and immunotherapy. Through the above research, we have provided a new biomarker for LGG prognosis prediction and more comprehensively explained the role of PSMB9 in the development of LGG. This study determined that PSMB9 can be used as an immunotherapy target through the analysis of immune data, providing new ideas for the clinical treatment of LGG.

Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes

Malignant gliomas derive from brain glial cells and represent >75% of primary brain tumors. This includes anaplastic astrocytoma (grade III; AS), the most common and fatal glioblastoma multiforme (grade IV; GBM), and oligodendroglioma (ODG). We have generated patient-derived AS, GBM, and ODG cell models to study disease mechanisms and test patient-centered therapeutic strategies. We have used an aptamer-based high-throughput SOMAscan^® 1.3K assay to determine the proteomic profiles of 1307 different analytes. SOMAscan^® proteomes of AS and GBM self-organized into closely adjacent proteomes which were clearly distinct from ODG proteomes. GBM self-organized into four proteomic clusters of which SOMAscan^® cluster 4 proteome predicted a highly inter-connected proteomic network. Several up- and down-regulated proteins relevant to glioma were successfully validated in GBM cell isolates across different SOMAscan^® clusters and in corresponding GBM tissues. Slow off-rate modified aptamer proteomics is an attractive analytical tool for rapid proteomic stratification of different malignant gliomas and identified cluster-specific SOMAscan^® signatures and functionalities in patient GBM cells.

Long non-coding RNA PSMA3-AS1 promotes glioma progression through modulating the miR-411-3p/HOXA10 pathway

BACKGROUND

Glioma is a common type of brain tumor and is classified as low and high grades according to morphology and molecules. Growing evidence has proved that long non-coding RNAs (lncRNAs) play pivotal roles in numerous tumors or diseases including glioma. Proteasome 20S subunit alpha 3 antisense RNA 1 (PSMA3-AS1), as a member of lncRNAs, has been disclosed to play a tumor-promoting role in cancer progression. However, the role of PSMA3-AS1 in glioma remains unknown. Therefore, we concentrated on researching the regulatory mechanism of PSMA3-AS1 in glioma.

METHODS

PSMA3-AS1 expression was detected using RT-qPCR. Functional assays were performed to measure the effects of PSMA3-AS1 on glioma progression. After that, ENCORI ( http://starbase.sysu.edu.cn/ ) database was used to predict potential genes that could bind to PSMA3-AS1, and miR-411-3p was chosen for further studies. The interaction among PSMA3-AS1, miR-411-3p and homeobox A10 (HOXA10) were confirmed through mechanism assays.

RESULTS

PSMA3-AS1 was verified to be up-regulated in glioma cells and promote glioma progression. Furthermore, PSMA3-AS1 could act as a competitive endogenous RNA (ceRNA) for miR-411-3p to regulate HOXA10 and thus affecting glioma progression.

CONCLUSION

PSMA3-AS1 stimulated glioma progression via the miR-411-3p/HOXA10 pathway, which might offer a novel insight for the therapy and treatment of glioma.

Does positive MGMT methylation outbalance the limitation of subtotal resection in glioblastoma IDH-wildtype patients?

Background

The impact on survival of complete resection (CR) in patients with malignant glioma and MGMT promoter methylation on adjuvant therapy strategies has been proven in the past. However, it is not known whether a MGMT promoter methylation can compensate a subtotal resection. Therefore, we analyzed the progress of postoperative residual tumor tissue depending on the molecular tumor status.

Methods

We included all glioblastoma, IDH-wildtype (WHO grade IV) patients with postoperative residual tumor tissue, who were treated at our neurooncological department between 2010 and 2018. Correlation of molecular patterns with clinical data and survival times was performed. The results were compared to patients following CR.

Results

267 patients with glioblastoma, IDH-wildtype (WHO grade IV) received surgery of whom 81 patients with residual tumor were included in the analysis. MGMT promoter was methylated in 31 patients (38.27%). Median OS and PFS were significantly increased in patients with methylated MGMT promoter (mOS: 16 M vs. 13 M, p = 0.009; mPFS: 13 M vs. 5 M, p = 0.003). In comparison to survival of patients following CR, OS was decreased in patients with residual tumor regardless MGMT methylation.

Conclusion

Our data confirm impact of MGMT promoter methylation in patients with glioblastoma, IDH-wildtype on OS and PFS. However, in comparison to patients after CR, a methylated MGMT promoter cannot compensate the disadvantage due to residual tumor volume. In terms of personalized medicine and quality of life as major goal in oncology, neuro-oncologists have to thoroughly discuss advantages and disadvantages of residual tumor volume versus possible neurological deficits in CR.

Myoinositol to Total Choline Ratio in Glioblastomas as a Potential Prognostic Factor in Preoperative Magnetic Resonance Spectroscopy

Isocitrate dehydrogenase (IDH) wild-type diffuse astrocytic tumors tend to be pathologically diagnosed as glioblastomas (GBMs). We previously reported that myoinositol to total choline (Ins/Cho) ratio in GBMs on magnetic resonance (MR) spectroscopy was significantly lower than that in IDH-mutant gliomas. We then hypothesized that a low Ins/Cho ratio is a poor prognosis factor in patients with GBMs, IDH-wild-type. In the present study, we calculated the Ins/Cho ratios of patients with GBMs and investigated their progression-free survival (PFS) and overall survival (OS) to determine their utility as prognostic marker. We classified patients with GBMs harboring wild-type IDH (n = 27) into two groups based on the Ins/Cho ratio, and compared patient backgrounds, pathological findings, PFS, OS, and copy number aberrations between the high and low Ins/Cho groups. Patients with GBMs in the low Ins/Cho ratio group indicated shorter PFS (P = 0.021) and OS (P = 0.048) than those in the high Ins/Cho group. Multivariate analysis demonstrated that the Ins/Cho ratio was significantly correlated with PFS (hazard ratio 0.24, P = 0.028). In conclusion, the preoperative Ins/Cho ratio can be used as a novel potential prognostic factor for GBM, IDH-wild-type.

A Candidate Prognostic Biomarker Complement Factor I Promotes Malignant Progression in Glioma

Objectives: Glioma is the most common and aggressive type of primary central nervous system (CNS) tumor in adults and is associated with substantial mortality rates. The aim of our study was to evaluate the prognostic significance and function of the complement factor I (CFI) in glioma.

Materials and Methods: The expression levels of CFI in glioma tissues and the survival of the CFI^high and CFI^low patient groups were analyzed using The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx). The correlation between CFI expression and clinicopathological features of glioma was determined by univariate and multivariate Cox regression analyses in the Chinese Glioma Genome Atlas (CGGA) database. The functional role of CFI in glioma was established through routine in vitro and in vivo assays.

Results: CFI is overexpressed in glioma and its high levels correlated with poor outcomes in both TCGA and CGGA datasets. Furthermore, CFI was identified as an independent prognostic factor of glioma in the CGGA database. CFI knockdown in glioma cell lines inhibited growth in vitro and in vivo, whereas its ectopic expression increased glioma cell proliferation, migration, and invasion in vitro. CFI protein levels were also significantly higher in the glioma tissues resected from patients and correlated to worse prognosis.

Conclusions: CFI is a potential prognostic biomarker in glioma and drives malignant progression.

Kiaa0101 serves as a prognostic marker and promotes invasion by regulating p38/snail1 pathway in glioma

Background

Kiaa0101, a regulator of cell proliferation, is overexpressed in many malignant tumors. However, its role in promoting invasion of glioma is poorly understood. Here, we investigated the effects of Kiaa0101 on glioma invasion and elucidated the underlying mechanisms of action.

Methods

We analyzed Kiaa0101 expression using datasets from four public databases, namely TCGA, CGGA, Gravendeel and Rembrandt as well as experimentally on 123 glioma samples via western blot (WB), RT-PCR and immunohistochemistry (IHC). We further quantified migration and invasion using wound healing and transwell assays. WB, IHC and immunofluorescence (IF) were used to detect expression of invasion related markers. Moreover, we detected tumor invasion of glioma cells in vivo in 5-week-old Balb/c nude mice.

Results

Kiaa0101 was upregulated in glioma, relative to non-tumor brain tissues, with the expression increasing with increase in glioma grade. Kiaa0101 mRNA expression was especially enriched in isocitrate dehydrogenase (IDH)1 wild-type glioma. Kaplan-Meier analysis, based on the aforementioned datasets, revealed that high Kiaa0101 levels were significantly associated with worse overall survival. Besides, shRNA-mediated Kiaa0101 knockdown inhibited migration and invasion of glioma cells by reducing snail1 expression both in vitro and in vivo, whereas its upregulation enhanced malignant behaviors of these cells. Furthermore, Kiaa0101 regulated snail1 expression by activating the p38MAPK signaling pathway.

Conclusions

Our findings strongly indicate that Kiaa0101 is a prognostic biomarker for malignant tumors, and its inhibition may be an effective strategy for treating glioma.

BATF2 prevents glioblastoma multiforme progression by inhibiting recruitment of myeloid-derived suppressor cells

The basic leucine zipper ATF-like transcription factor 2 (BATF2) has been implicated in inflammatory responses and anti-tumour effects. Little, however, is known regarding its extracellular role in maintaining a non-supportive cancer microenvironment. Here, we show that BATF2 inhibits glioma growth and myeloid-derived suppressor cells (MDSCs) recruitment. Interestingly, extracellular vesicles (EVs) from BATF2-overexpressing glioma cell lines (BATF2-EVs) inhibited MDSCs chemotaxis in vitro. Moreover, BATF2 inhibited intracellular SDF-1α and contributes to decreased SDF-1α in EVs. In addition, BATF2 downregulation-induced MDSCs recruitment were reversed by blocking SDF-1α/CXCR4 signalling upon AMD3100 treatment. Specifically, detection of EVs in 24 pairs of gliomas and healthy donors at different stages revealed that the abundance of BATF2-positive EVs in plasma (BATF2⁺ plEVs) can distinguish stage III-IV glioma from stage I-II glioma and healthy donors. Taken together, our study identified novel regulatory functions of BATF2 in regulating MDSCs recruitment, providing a prognostic value in terms of the number of BATF2⁺ plEVs in glioma stage.

Management, outcomes, and prognostic factors of adult primary spinal cord gliomas

PURPOSE

Primary spinal cord tumors are rare, particularly in the adult population, and national guidelines remain ambiguous with regard to management approaches. To address this knowledge gap, we evaluated management, outcomes, and prognostic factors of these neoplasms.

METHODS

The National Cancer Database was queried (2004-2016) for newly-diagnosed, histologically-confirmed WHO grades I-III astrocytomas and glioblastoma. Statistics included Kaplan-Meier overall survival (OS) analysis, along with Cox proportional hazards modeling.

RESULTS

Of 1,033 subjects, 196 (19%) were pilocytic astrocytomas (PAs), 539 (52%) were grade II/III astrocytomas, and 298 (29%) were glioblastomas (GBMs). Respectively, 11%, 30%, and 27% did not undergo resection (biopsy only). RT was delivered to 27%, 54%, and 73%; chemotherapy was given to 5%, 21%, and 37%, respectively. The median OS was not reached for PAs, but was 101.2 months for grade II/III astrocytomas, and 23.9 months for GBMs (p < 0.001). Neither chemotherapy nor RT (or dose thereof) was associated with increased OS for grade II/III astrocytomas (p > 0.05 for all), though there was a trend toward improved OS with the use of chemotherapy for patients with GBM. Surgical resection was associated with improved OS for grade II/III astrocytomas and GBM (p < 0.05). Independent prognostic factors for survival in this cohort included histologic classification and resection (compared to biopsy only) (p < 0.05 for both).

CONCLUSIONS

This study sheds light onto the management of these rare tumors; surgery was associated with OS benefit for patients with GBM and Grade II/III astrocytomas. Neither RT nor chemotherapy were associated with OS benefit. Although not implying causation, these data can be used to guide patient counseling and therapeutic approaches.

Long noncoding RNA HNF1A-AS1 regulates proliferation and apoptosis of glioma through activation of the JNK signaling pathway via miR-363-3p/MAP2K4

Long noncoding RNAs (lncRNAs) have been proven to exert important functions in the various biological processes of human cancers. It has been reported that lncRNA HNF1 homeobox A antisense RNA 1 (HNF1A-AS1) was abnormally expressed and played a role in the initiation and development of various human cancers. In this study, we confirmed that the expression level of HNF1A-AS1 was increased in glioma tissues and cells. Knockdown of HNF1A-AS1 inhibited cell proliferation and promoted cell apoptosis in glioma. Then, we disclosed the downregulation of miR-363-3p in glioma tissues and cell lines. The interaction between HNF1A-AS1 and miR-363-3p was identified in glioma cells. Furthermore, an inverse correlation between HNF1A-AS1 and miR-363-3p was observed in glioma tissues. Afterwards, we recognized that MAP2K4 was a direct target of miR-363-3p. The expression of MAP2K4 was negatively correlated with miR-363-3p while positively related to HNF1A-AS1 in glioma tissues. We also found the regulatory effect of HNF1A-AS1 on the MAP2K4-dependent JNK signaling pathway. All findings indicated that HNF1A-AS1 induces the upregulation of MAP2K4 to activate the JNK signaling pathway to promote glioma cell growth by acting as a miR-363-3p sponge.

Large-Scale Analysis Reveals the Specific Clinical and Immune Features of DGCR5 in Glioma

Purpose

Long non-coding RNA DGCR5 plays different roles in different types of cancer. The purpose of this study was to investigate the clinicopathological features, potential biological functions and prognostic significance of DGCR5 in glioma in a large-scale study.

Materials and Methods

A total of 697 RNA-seq data from The Cancer Genome Atlas (TCGA) and 301 mRNA microarray data from Chinese Glioma Genome Atlas (CGGA) were enrolled in this study. R language was used as the main tool for statistical analysis and graphical work.

Results

DGCR5 showed a negative correlation with the WHO grade of malignancy in glioma. Specifically, DGCR5 expression was significantly decreased in GBM and IDH wild-type glioma. Gene ontology analysis showed that DGCR5 was predominantly enriched in immune-related biological processes. Additionally, DGCR5 showed a significant correlation with stromal and immune cell populations, inflammatory activities and immune checkpoints. Clinically, patients with low-expression level of DGCR5 exhibited a worse overall survival.

Conclusion

DGCR5 expression is downregulated in glioma, and low DGCR5 independently predicts worse prognosis in glioma patients. Moreover, DGCR5 is significantly associated with immune response and immune infiltration. These findings suggest that DGCR5 is a promising immunotherapy target and a novel prognostic biomarker for glioma.

Rare Cases of IDH1 Mutations in Spinal Cord Astrocytomas

A low occurrence rate of spinal cord gliomas (4.3% of primary and glial CNS tumors) and the associated difficulties in building statistically significant cohorts of patients considerably slow down the development of effective approaches to the treatment of spinal cord tumors compared to brain tumors. Despite our extensive knowledge regarding IDH mutations in intracranial tumors, mutations of this gene in spinal cord astrocytomas remain poorly understood. In this study, we report on five cases of identified mutations in the IDH1 gene in spinal cord astrocytoma cells, two of which are unique, as they have never been previously described in CNS gliomas.

From astrocytoma to glioblastoma: a clonal evolution study

Astrocytomas often recur after surgical resection, but the underlying mechanism remains enigmatic. Elucidation of clonal evolution in primary and relapse tumors may provide important information on tumor progression. Here, we examined genetic factors underlying recurrence in a patient with astrocytoma initially diagnosed with World Health Organization (WHO) grade II astrocytoma, who then relapsed with glioblastoma (WHO grade IV) complicated with local anaplastic astrocytoma (WHO grade III). We performed genomic DNA sequencing and data analysis of paired tumor tissue specimens and a peripheral blood sample (control), and used expands software for subclone analysis. A germline NOTCH1 missense mutation was identified in the peripheral blood sample, the primary tumor and the relapse tumor; in addition, we identified a tumor protein p53 (TP53) heterozygous nonsense mutation in the primary tumor and a TP53 homozygous nonsense mutation and an IDH1 heterozygous missense mutation in the relapse tumor. Clonal evolution trees indicated higher heterogeneity in the relapse tumor. Although germline mutations might contribute to the driving force of the primary tumor, aggressive chemotherapy and radiation may apply selective pressure for tumor clonal evolution; furthermore, a total loss of function of gatekeeping genes (TP53) may result in impaired DNA repair and catastrophic chromosomal aberrations.

Molecular Biomarkers of Brain and Spinal Cord Astrocytomas

Spinal cord astrocytomas are rare diseases of the central nervous system. The localization of these tumors and their infiltrative growth complicate their surgical resection, increase the risk of postoperative complications, and require more careful use of radio- and chemotherapy. The information on the genetic mutations associated with the onset and development of astrocytomas provides a more accurate neoplasm diagnosis and classification. In some cases, it also allows one to determine the optimal methods for treating the neoplasm, as well as to predict the treatment outcomes and the risks of relapse. To date, a number of molecular markers that are associated with brain astrocytomas and possess prognostic value have been identified and described. Due to the significantly lower incidence of spinal cord astrocytomas, the data on similar markers are much more sparse and are presented with a lesser degree of systematization. However, due to the retrospective studies of clinical material that have been actively conducted abroad in recent years, the formation of statistically significant genetic landscapes for various types of tumors, including intradural spinal cord tumors, has begun. In this regard, the purpose of this review is to analyze and systematize the information on the most significant genetic mutations associated with various types of astrocytomas, as well as discuss the prospects for using the corresponding molecular markers for diagnostic and prognostic purposes.

Targeted next-generation sequencing panel (TruSight Tumor 170) in diffuse glioma: a single institutional experience of 135 cases

PURPOSE

The TruSight Tumor 170 (TST-170) panel consists of a DNA workflow for the identification of single-nucleotide variants, small insertions and deletions, and copy number variation, as well as a panel of 55 genes for a RNA workflow for the identification of splice variants and gene fusions. To date, the application of TST-170 in diffuse gliomas (DGs) has not been described.

METHODS

We analyzed 135 samples of DG, which were diagnosed by WHO criteria based on histological features and conventional molecular tests including immunostaining, 1p/19q FISH, and analysis of MGMT methylation and TERT promoter mutation.

RESULTS

A total of 135 cases consisted of 38 IDH-mutant [17 astrocytoma (AC), 13 oligodendroglioma (OD) and eight glioblastoma (GBM)], 87 IDH-wildtype (six AC, three OD and 78 GBM), and 10 diffuse midline glioma, H3K27M-mutant. DNA analysis enabled the detection of all mutations identified in these samples by conventional techniques, and the results were highly comparable to the known mutations in each subtype. RNA analysis detected four fusion genes including PTPRZ1-MET, FGFR3-TACC3, FAM131B-BRAF, and RET-CCDC6 and one splicing variant (EGFR vIII mutant). Clustered copy number loss in 1p and 19q loci genes were detected in 1p/19q-codeleted OD.

CONCLUSIONS

The application of TST-170 panel based NGS in clinical and laboratory setting is expected to improve diagnostic accuracy and prognostication. Most benefits are expected in IDH-wildtype DG, a group of genetically heterogenous tumors harboring DNA sequence changes, copy number alterations, and fusions in a large number of oncogenes and tumor suppressor genes.

Specific clinical and immune features of CD68 in glioma via 1,024 samples

Background

There is a growing recognition that tumor-associated macrophages (TAMs) are recruited to the glioma environment, facilitating tumor proliferation and migration by creating an immunosuppressive microenvironment. CD68 has been widely reported as a specific marker of TAMs in cancer.

Purpose

To clarify the role of CD68 in glioma, we investigated its function at the transcriptome level and relationship with clinical practice.

Patients and methods

In total, 325 RNA-seq data from Chinese Glioma Genome Atlas (CGGA) and 697 RNA-seq data from The Cancer Genome Atlas (TCGA) network were enrolled in this study. CD68-specific findings were further analyzed with R language, and the prognostic impacts were validated through analyzing the overall survival (OS).

Results

CD68 showed a positive correlation with the WHO grade of malignancy in glioma. Meanwhile, CD68 was predominantly expressed in IDH wide type and mesenchymal subtype. Gene ontology (GO) analysis revealed that CD68-related genes were closely related to inflammatory response and immune response. Moreover, seven cultures of metagenes further confirmed that CD68 was a specific marker for macrophages in inflammatory response and played an important role in suppressing T-cell-mediated immunity. The Pearson correlation test suggested that CD68 showed robust correlation with other markers of macrophages and immune checkpoints, including PD-1 and TIM-3. Clinically, a high expression level of CD68 in tumors exhibited a poor survival in glioma patients.

Conclusion

Our results demonstrated that CD68 acted as an immune suppressor and contributed to glioma progression in the tumor microenvironment. These findings may expand our understanding of CD68-specific clinical and immune features in glioma.

CKAP2 expression is associated with glioma tumor growth and acts as a prognostic factor in high‑grade glioma

Cytoskeletal‑associated protein 2 (CKAP2), which is also known as tumor‑associated microtubule‑associated protein, has been reported to be dysregulated in various types of human cancer. However, the role of CKAP2 in glioma has not been fully elucidated. The present study evaluated the expression pattern of CKAP2 using the Chinese Glioma Genome Atlas microarray database, which included 301 patients, and validated the findings using The Cancer Genome Atlas RNA sequencing database. Kaplan‑Meier survival analysis, and univariate and multivariate Cox analyses, were used to estimate survival distributions. Furthermore, the biological implication of aberrant CKAP2 expression in high‑grade glioma (HGG) was investigated using Gene Ontology analysis, gene set enrichment analysis, gene set variation analysis and STRING. The results indicated that patients with HGG exhibited significantly higher CKAP2 expression levels compared with patients with low‑grade glioma in both databases. Higher expression levels of CKAP2 were significantly associated with shorter overall survival and progression‑free survival of patients with HGG. Furthermore, CKAP2 was also positively correlated with known malignant factors, including high Ki67 expression and phosphatase and tensin homolog mutations. The univariate and multivariate Cox regression analyses demonstrated that CKAP2 may be a novel independent prognostic biomarker for patients with HGG. Functional assays also indicated that CKAP2 was closely associated with the cell cycle, mitosis and cell proliferation. These results suggested that CKAP2 may be associated with tumor growth and could serve as an independent prognostic factor, particularly in patients with HGG.

The prognostic value of DAPK1 hypermethylation in gliomas: A site-specific analysis

BACKGROUND AND AIMS

The gene of death associated protein kinase 1 (DAPK1) has been reported to be methylated in various cancers including gliomas. However, its prognostic value for gliomas is still controversy, and the methylation at specific CpG sites of DAPK1 has not been investigated. The aim of this study was to prognostically evaluate the methylation level of different CpG sites within DAPK1 promoter region in gliomas.

METHODS

Based on sodium bisulfite treated DNA products, we made use of DNA pyrosequencing method to evaluate overall and site-specific methylation of DAPK1 in 143 gliomas and 26 benign tumors (meningeomas) or normal brain tissues. We both statistically analyzed the association between methylation levels of each CpG site and the clinicopathological characteristics, and estimated the prognosis predictive value of site-specific methylation for glioma patients.

RESULTS

Methylation status of DAPK1 site -1527, -1543, and the overall five sites concerned was higher in gliomas than controlled subjects (p < 0.001). Hypermethylation at site -1527 or together with site -1543 associated with better survival in patients taken postoperative therapies (-1527: p = 0.002; -1527 & -1543: p = 0.023), as well as in patients just underwent radiotherapy after surgery (-1527: p = 0.015; -1527 & -1543: p = 0.030). However, Cox regression analysis indicated the site-specific methylation was not independent contributor for gliomas prognosis.

CONCLUSION

Analysis of DAPK1 gene promoter by quantitative pyrosequencing provided more detailed information of methylation status of CpG sites. DAPK1 methylation level is associated with gliomas clinical features and outcomes. Interestingly, the hypermethylation at site -1527 or together with site -1543 indicated good sensitivity of postoperative therapies, especially radiotherapy. Thus, site specifically analysis of DAPK1 methylation may be a valuable diagnostic and prognostic estimation for gliomas.

Seizures at presentation are correlated with better survival outcomes in adult diffuse glioma: A systematic review and meta-analysis

PURPOSE

Seizures are the most common presenting sign of patients with diffuse glioma. In the current study, we performed a meta-analysis to determine the correlation of seizures at presentation to survival outcomes in adult diffuse glioma, and the possible mechanisms were also discussed.

METHODS

A comprehensive literature search was performed in PUBMED, EMBASE, Web of Science and the Cochrane Central Register of Controlled Trials. The pooled hazard ratio (HR) and corresponding 95% confidence interval (CI) were used to estimate effects. Heterogeneity among studies and publication bias were also evaluated.

RESULTS

11 studies with 2088 patients were finally included for the current meta-analysis. Seizure-free preoperatively was significantly associated with a poor overall survival in patients with diffuse glioma, the pooled HR was 1.73 (95% CI 1.43-2.08, Z = 5.71, p < 0.001). Subgroup analysis was also performed by tumor grade, the same association was identified in both low-grade glioma (pooled HR 2.49, 95% CI 1.47-4.20, Z = 3.40, p < 0.001) and glioblastoma (pooled HR 1.46, 95% CI 1.27-1.68, Z = 5.24, p < 0.001). A significant correlation of seizure-free with a poor progression-free survival was also identified (pooled HR 1.42, 95% CI 1.06-1.92, Z = 2.33, p = 0.02), although only 3 studies comprising 368 patients were included.

CONCLUSION

The current study determined that seizures at presentation were an independent predictor of better survival outcomes in adult diffuse glioma. It is the first study which provides a comprehensive standardized assessment of the association between seizures at presentation with long-term survival outcomes in patients with diffuse glioma.

Single-Cell RNA-Sequencing in Glioma

PURPOSE OF REVIEW

In this review, we seek to summarize the literature concerning the use of single-cell RNA-sequencing for CNS gliomas.

RECENT FINDINGS

Single-cell analysis has revealed complex tumor heterogeneity, subpopulations of proliferating stem-like cells and expanded our view of tumor microenvironment influence in the disease process. Although bulk RNA-sequencing has guided our initial understanding of glioma genetics, this method does not accurately define the heterogeneous subpopulations found within these tumors. Single-cell techniques have appealing applications in cancer research, as diverse cell types and the tumor microenvironment have important implications in therapy. High cost and difficult protocols prevent widespread use of single-cell RNA-sequencing; however, continued innovation will improve accessibility and expand our of knowledge gliomas.

IDH1 mutation is associated with a higher preoperative seizure incidence in low-grade glioma: A systematic review and meta-analysis

PURPOSE

Gliomas, particularly low-grade gliomas (LGGs), are highly epileptogenic. Seizure is the most common presenting sign of LGG patients and significantly decreases their quality of life. Accordingly, there is a need for a better understanding of the mechanisms and risk factors of glioma-related epilepsy. The current study aimed to perform a comprehensive meta-analysis to investigate the correlation of isocitrate-dehydrogenase 1 (IDH1), an important molecular biomarker for glioma classification and prognosis, to preoperative seizure incidence in LGG.

METHODS

PUBMED, EMBASE, and Web of Science databases were searched for relevant studies. The odds ratio (OR) and corresponding 95% confidence interval (CI) were used as the primary measures to assess the correlation between IDH1 mutation and preoperative seizure incidence.

RESULTS

A total of 722 LGG patients, including 555 patients with IDH1 mutation and 167 patients with wild-type IDH1 were enrolled in the current meta-analysis. The pooled OR was 2.47 (95% CI 1.70-3.57, Z = 4.78, p < 0.01). No significant heterogeneity was observed among all included studies and no publication bias was identified.

CONCLUSION

The current meta-analysis identified that IDH1 mutation was correlated to a higher preoperative seizure incidence in LGG. This result would generate impetus for research on the mechanisms behind this correlation, and provide a new idea for the individualized treatment of glioma-related epilepsy.

Molecular alterations in pediatric brainstem gliomas

BACKGROUND

Diffuse intrinsic pontine gliomas (DIPGs) have a dismal prognosis. Previously, diagnosis was based on a typical clinical presentation and magnetic resonance imaging findings. After the start of the era of biopsies, DIPGs bearing H3 K27 mutations have been reclassified into a novel entity, diffuse midline glioma, based on the presence of this molecular alteration. However, it is not well established how clinically diagnosed DIPG overlap with H3 K27-mutated diffuse midline gliomas, and whether rare long-term survivors also belong to this group.

METHODS

We studied tumor samples obtained at diagnosis or upon autopsy from 23 children, including two long-term survivors. Based on clinical, radiological, and histological findings, all tumors were previously diagnosed as DIPGs. All samples were analyzed for genetic alterations by next-generation sequencing (NGS) and for protein expression by immunohistochemistry (IHC).

RESULTS

H3 K27 was mutated in NGS or IHC in 20 patients, excluding both long-term survivors. One of these long-term survivors harbored a mutation in IDH1, formerly considered to be an alteration absent in pediatric diffuse brainstem gliomas. Other altered genes in NGS included TP53 (10 patients), MET and PDGFRA (3 patients each), VEGFR and SMARCA4 (2 patients each), and PPARγ, PTEN and EGFR in 1 patient, respectively. IHC revealed cMYC expression in 15 of 24 (63%) of all samples, exclusively in the biopsies.

CONCLUSIONS

Eighty-seven percent of the tumors formerly diagnosed as DIPGs could be reclassified as H3 K27-mutated diffuse midline gliomas. Both long-term survivors lacked this alteration. Contrary to former conceptions, IDH1 mutations may occur also in pediatric brainstem gliomas.

Neuroglobin promotes the proliferation and suppresses the apoptosis of glioma cells by activating the PI3K/AKT pathway

Our previous study demonstrated that neuroglobin (Ngb) functions as an independent predictive indicator of the prognosis of patients with glioma and promotes cancer cell growth by suppressing apoptosis. However, the understanding of the mechanisms underlying the survival‑enhancing function of Ngb in glioma is limited. In the present study, KEGG PathwayFinder by gene correlation analysis was performed on the R2: Genomics Analysis and Visualization Platform, which revealed a high association between Ngb and the phosphatidylinositol 3‑kinase (PI3K)/AKT pathway using glioma data (GSE4290) from the Gene Expression Omnibus database. Furthermore, western blotting experiments were performed in U251 and U87 glioma cells, and Ngb knockdown using short hairpin RNA reduced the protein levels of phosphorylated (p)‑AKT, p‑mammalian target of rapamycin (mTOR) and antiapoptotic factor Bcl‑2, and increased the expression of the proapoptotic protein Bcl‑2‑associated X, in U251 cells. In addition, Ngb overexpression promoted the activation of the PI3K/AKT pathway in U87 cells. MK2206, a PI3K/AKT signaling inhibitor, reduced the expression of p‑AKT and increased the levels of apoptosis‑associated proteins, including cleaved poly(ADP‑ribose) polymerase 1 and cleaved caspase‑3/7/8, in Ngb‑overexpressing U87 cells. Furthermore, MK2206 treatment reduced the proliferation and induced the apoptosis of Ngb‑overexpressing U87 cells, as indicated by the results of MTT, colony formation and flow cytometry assays. In addition, insulin‑like growth factor‑1, a PI3K/AKT signaling activator, reversed Ngb knockdown‑induced growth arrest and apoptosis in U251 cells. In conclusion, the results of the present study indicate that Ngb may facilitate a malignant phenotype of glioma cells by activating the PI3K/AKT pathway.

LncRNA HSP90AA1-IT1 promotes gliomas by targeting miR-885-5p-CDK2 pathway

It is well established that ncRNAs are emerging as important regulators in various types of cancers, however, their functions and contributions in cancers remain insufficiently defined. In this study, we reported the expression levels of a long noncoding RNA (lncRNA), named HSP90AA1-IT1 (HSP90AA1 intronic transcript 1), appeared to correlate with the pathological grades of gliomas and high level of HSP90AA1-IT1 indicated poor prognosis. Downregulation of HSP90AA1-IT1 in the glioma cell lines significantly suppressed cell viability, proliferation, EMT, invasion and migration in addition to an increase in apoptosis and aberrant cell cycle progression. The tumorigenic capacity of these cells in vivo were also inhibited. We further demonstrated that the oncogenic effects of HSP90AA1-IT1 could be mediated by a direct binding to miR-885-5p. Sharing the same binding sites with CDK2, a key regulator in gliomagenesis, HSP90AA1-IT1 competitively bound to miR-885-5p, thereby prevented CDK2 from miR-885-5p mediated post-transcriptional repression. Taken together, it is concluded that HSP90AA1-IT1, performs its function via regulating the development of gliomas through miR-885-5p-CDK2 signaling axis, and this has added new perspective to its role in tumorigenesis, thus providing potential therapeutic targets for glioma treatment.

Genome-wide ChIP-seq analysis of EZH2-mediated H3K27me3 target gene profile highlights differences between low- and high-grade astrocytic tumors

Enhancer of zeste homolog-2(EZH2) is a key epigenetic regulator that functions as oncogene and also known for inducing altered trimethylation of histone at lysine-27 (H3K27me3) mark in various tumors. However, H3K27me3 targets and their precise relationship with gene expression are largely unknown in astrocytic tumors. In this study, we checked EZH2 messenger RNA and protein expression in 90 astrocytic tumors of different grades using quantitative PCR and immunohistochemistry, respectively. Further, genome-wide ChIP-seq analysis for H3K27me3 modification was also performed on 11 glioblastomas (GBMs) and 2 diffuse astrocytoma (DA) samples. Our results showed EZH2 to be highly overexpressed in astrocytic tumors with a significant positive correlation with grade. Interestingly, ChIP-seq mapping revealed distinct differences in genes and pathways targeted by these H3K27me3 modifications between GBM versus DA. Neuroactive ligand receptor pathway was found most enriched in GBM (P = 9.4 × 10-25), whereas DA were found to be enriched in metabolic pathways. Also, GBM showed a higher enrichment of H3K27me3 targets reported in embryonic stem cells and glioma stem cells as compared with DAs. Our results show majority of these H3K27me3 target genes were downregulated, not only due to H3K27me3 modification but also due to concomitant DNA methylation. Further, H3K27me3 modification-associated gene silencing was not restricted to promoter but also present in gene body and transcription start site regions. To the best of our knowledge, this is the first high-resolution genome-wide mapping of H3K27me3 modification in adult astrocytic primary tissue samples of human, highlighting the differences between grades. Interestingly, we identified SLC25A23 as important target of H3K27me3 modification, which was downregulated in GBM and its low expression was associated with poor prognosis in GBMs.

miR-489 inhibits proliferation, cell cycle progression and induces apoptosis of glioma cells via targeting SPIN1-mediated PI3K/AKT pathway

microRNA-489 (miR-489), a newly identified tumor-related miRNA, functions as an oncogene or tumor suppressor via regulating growth and metastasis of human cancers. But, the clinical significance, biological function and underlying mechanisms of miR-489 in glioma remain rarely known. Here, we showed that the levels of miR-489 in glioma tissues were notably underexpressed compared to corresponding non-tumor tissues. In accordance, the relative levels of miR-489 were decreased in glioma cell lines compared with NHA cells. Kaplan-Meier plots indicated that miR-489 low expressing glioma patients showed a prominent shorter overall survival. In addition, miR-489 overexpression prohibited proliferation and cell cycle progression, and promoted apoptosis in U251 cells. While, miR-489 knockdown showed opposite effects on these cellular processes of U87 cells. In vivo experiments demonstrated that miR-489 restoration reduced the tumor volume and weight of subcutaneous glioma xenografts in nude mice. Notably, Spindlin 1 (SPIN1) was inversely and directly regulated by miR-489 in glioma cells. A negative correlation between the expression of miR-489 and SPIN1 mRNA was confirmed in glioma tissues. Interestingly, miR-489 inversely modulated activation of PI3K/AKT pathway and expression of downstream targets including p-mTOR, Cyclin D1 and BCL-XL. SPIN1 re-expression abolished the effects of miR-489 on U251 cells with enhanced activation of PI3K/AKT pathway and malignant phenotype. Meanwhile, AKT inhibitor MK-2206 blocked activation of PI3K/AKT pathway and resulted in reduced proliferation, cell cycle arrest and increased apoptosis in miR-489 down-regulating U87 cells. Altogether, our data support that miR-489 loss facilitates malignant phenotype of glioma cells probably via SPIN1-mediated PI3K/AKT pathway.

Diagnostic and Therapeutic Biomarkers in Glioblastoma: Current Status and Future Perspectives

Glioblastoma (GBM) is a primary neuroepithelial tumor of the central nervous system, characterized by an extremely aggressive clinical phenotype. Patients with GBM have a poor prognosis and only 3–5% of them survive for more than 5 years. The current GBM treatment standards include maximal resection followed by radiotherapy with concomitant and adjuvant therapies. Despite these aggressive therapeutic regimens, the majority of patients suffer recurrence due to molecular heterogeneity of GBM. Consequently, a number of potential diagnostic, prognostic, and predictive biomarkers have been investigated. Some of them, such as IDH mutations, 1p19q deletion, MGMT promoter methylation, and EGFRvIII amplification are frequently tested in routine clinical practice. With the development of sequencing technology, detailed characterization of GBM molecular signatures has facilitated a more personalized therapeutic approach and contributed to the development of a new generation of anti-GBM therapies such as molecular inhibitors targeting growth factor receptors, vaccines, antibody-based drug conjugates, and more recently inhibitors blocking the immune checkpoints. In this article, we review the exciting progress towards elucidating the potential of current and novel GBM biomarkers and discuss their implications for clinical practice.

Beyond Alkylating Agents for Gliomas: Quo Vadimus?

Recent advances in therapies have yielded notable success in terms of improved survival in several cancers. However, such treatments have failed to improve outcome in patients with gliomas for whom surgery followed by radiation therapy and chemotherapy with alkylating agents remain the standard of care. Genetic and epigenetic studies have helped identify several alterations specific to gliomas. Attempts to target these altered pathways have been unsuccessful due to various factors, including tumor heterogeneity, adaptive resistance of tumor cells, and limitations of access across the blood-brain barrier. Novel therapies that circumvent such limitations have been the focus of intense study and include approaches such as immunotherapy, targeting of signaling hubs and metabolic pathways, and use of biologic agents. Immunotherapeutic approaches including tumor-targeted vaccines, immune checkpoint blockade, antibody-drug conjugates, and chimeric antigen receptor-expressing cell therapies are in various stages of clinical trials. Similarly, identification of key metabolic pathways or converging hubs of signaling pathways that are tumor specific have yielded novel targets for therapy of gliomas. In addition, the failure of conventional therapies against gliomas has led to a growing interest among patients in the use of alternative therapies, which in turn has necessitated developing evidence-based approaches to the application of such therapies in clinical studies. The development of these novel approaches bears potential for providing breakthroughs in treatment of more meaningful and improved outcomes for patients with gliomas.

B-cell CLL/lymphoma 3 promotes glioma cell proliferation and inhibits apoptosis through the oncogenic STAT3 pathway

Aberrant expression of oncogenes and/or tumor suppressors play fundamental roles in the pathogenesis of glioma. B-cell CLL/lymphoma 3 (BCL3) was previously found to be a putative proto-oncogene in human cancers and the decoy receptor DcR1 is induced in a p50/Bcl3-dependent manner and attenuates the efficacy of temozolomide in glioblastoma cells. However, its expression status, clinical significance and biological functions in glioma remain largely unknown. In the present study, the levels of BCL3 were overexpressed in glioma compared to normal brain tissues. Furthermore, high expression of BCL3 protein was confirmed by immunoblotting in glioma cells as compared with normal human astrocyte cell line. The positive expression of BCL3 was correlated with adverse prognostic features and reduced overall survival rate of glioma patients. BCL3 silencing resulted in prominent decreased proliferation, cell cycle arrest in G1 phase and increased apoptosis in U251 cells. In contrast, BCL3 overexpression in U87 cells remarkably facilitated proliferative ability and cell cycle progression and induced apoptosis. In vivo studies showed that BCL3 knockdown inhibited the tumor growth of U251 cells in a mouse xenograft model. Mechanistically, BCL3 positively regulated the abundance of STAT3, p-STAT3 and the downstream targets of STAT3 pathway including BCL2, MCL-1 and cyclin D1 in glioma cells. Furthermore, a positive correlation between BCL3 and STAT3 expression was observed in glioma specimens. Notably, we confirmed that STAT3 knockdown abolished the oncogenic roles of BCL3 in glioma. In conclusion, we suggest that BCL3 serves as an oncogene in glioma by modulating proliferation, cell cycle progression and apoptosis, and its oncogenic effects are mediated by the STAT3 signaling pathway.

Long non-coding RNA TUG1 acts as a miR-26a sponge in human glioma cells

BACKGROUND

Long non-coding RNA taurine upregulated gene 1 (TUG1) acts as an important regulator in cancer pathogenesis; however, its functional mechanism in glioma development remains unclear. This study aims to explore the potential function of TUG1 in glioma by sponging miR-26a.

METHODS

The expression of TUG1, miR-26a, and phosphatase and tensin homolog (PTEN) in 20 paired glioma tissues was detected by quantitative real-time PCR and subjected to correlation analysis. Bioinformatics analysis was performed by using DIANA Tools. Abnormal TUG1 expression was conducted in two glioma cells to analyze its regulation on miR-26a and PTEN using real-time PCR, western blot, and luciferase reporter assay.

RESULTS

TUG1 expression was confirmed to be upregulated in glioma tissues, and showed an inverse correlation with downregulated miR-26a. TUG1 could negatively regulate the expression of miR-26a in glioma cells. The bioinformatics prediction revealed putative miR-26a binding sites within TUG1 transcripts. Further experiments demonstrated the positive regulation of TUG1 on the miR-26a target, PTEN, wherein TUG1 could inhibit the negative regulation of miR-26a on PTEN by binding its 3'UTR. Additionally, the expression of PTEN was also upregulated in glioma tissues, showing a positive or negative correlation with TUG1 or miR-26a, respectively.

CONCLUSION

TUG1 could serve as a miR-26a sponge in human glioma cells, contributing to the upregulation of PTEN. This study revealed a new TUG1/miR-26a/PTEN regulatory mechanism and provided a further understanding of the tumor-suppressive role of TUG1 in glioma development.

Prognostic role of IDH mutations in gliomas: a meta-analysis of 55 observational studies

Background

IDH (Isocitrate dehydrogenase) mutations occur frequently in gliomas, but their prognostic impact has not been fully assessed. We performed a meta-analysis of the association between IDH mutations and survival in gliomas.

Methods

Pubmed and EMBASE databases were searched for studies reporting IDH mutations (IHD1/2 and IDH1) and survival in gliomas. The primary outcome was overall survival (OS); the secondary outcome was progression-free survival (PFS). Hazard ratios (HR) with 95% confidence interval (CI) were determined using the Mantel-Haenszel random-effect modeling. Funnel plot and Egger's test were conducted to examine the risk of publication bias.

Results

Fifty-five studies (9487 patients) were included in the analysis. Fifty-four and twenty-seven studies investigated the association between IDH1/2 mutations and OS/PFS respectively in patients with glioma. The results showed that patients possessing an IDH1/2 mutation had significant advantages in OS (HR = 0.39, 95%CI: 0.34–0.45; P < 0.001) and PFS (HR = 0.42, 95% CI: 0.35–0.51; P < 0.001). Subgroup analysis showed a consistent result with pooled analysis, and patients with glioma of WHO grade III or II-III had better outcomes.

Conclusions

These findings provide further indication that patients with glioma harboring IDH mutations have improved OS and PFS, especially for patients with WHO grade III and grade II-III.

Design, synthesis, and evaluation of cisplatin-containing EGFR targeting bioconjugates as potential therapeutic agents for brain tumors

The aim of this study was to evaluate four different platinated bioconjugates containing a cisplatin (cis-diamminedichloroplatinum [cis-DDP]) fragment and epidermal growth factor receptor (EGFR)-targeting moieties as potential therapeutic agents for the treatment of brain tumors using a human EGFR-expressing transfectant of the F98 rat glioma (F98_EGFR) to assess their efficacy. The first two bioconjugates employed the monoclonal antibody cetuximab (C225 or Erbitux^®) as the targeting moiety, and the second two used genetically engineered EGF peptides. C225-G₅-Pt was produced by reacting cis-DDP with a fifth-generation polyamidoamine dendrimer (G₅) and then linking it to C225 by means of two heterobifunctional reagents. The second bioconjugate (C225-PG-Pt) employed the same methodology except that polyglutamic acid was used as the carrier. The third and fourth bioconjugates used two different EGF peptides, PEP382 and PEP455, with direct coordination to the Pt center of the cis-DDP fragment. In vivo studies with C225-G₅-Pt failed to demonstrate therapeutic activity following intracerebral (ic) convection-enhanced delivery (CED) to F98_EGFR glioma-bearing rats. The second bioconjugate, C225-PG-Pt, failed to show in vitro cytotoxicity. Furthermore, because of its high molecular weight, we decided that lower molecular weight peptides might provide better targeting and microdistribution within the tumor. Both PEP382-Pt and PEP455-Pt bioconjugates were cytotoxic in vitro and, based on this, a pilot study was initiated using PEP455-Pt. The end point for this study was tumor size at 6 weeks following tumor cell implantation and 4 weeks following ic CED of PEP455-Pt to F98 glioma-bearing rats. Neuropathologic examination revealed that five of seven rats were either tumor-free or only had microscopic tumors at 42 days following tumor implantation compared to a mean survival time of 20.5 and 26.3 days for untreated controls. In conclusion, we have succeeded in reformatting the toxicity profile of cis-DDP and demonstrated the therapeutic efficacy of the PEP455-Pt bioconjugate in F98 glioma-bearing rats.

Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors

BACKGROUND

Identification of genetic changes in CNS tumors is important for the appropriate clinical management of patients. Our objective was to develop a next-generation sequencing (NGS) assay for simultaneously detecting the various types of genetic alterations characteristic for adult and pediatric CNS tumors that can be applied to small brain biopsies.

METHODS

We report an amplification-based targeted NGS assay (GlioSeq) that analyzes 30 genes for single nucleotide variants (SNVs) and indels, 24 genes for copy number variations (CNVs), and 14 types of structural alterations in BRAF, EGFR, and FGFR3 genes in a single workflow. GlioSeq performance was evaluated in 54 adult and pediatric CNS tumors, and the results were compared with fluorescence in-situ hybridization, Sanger sequencing, and reverse transcription PCR.

RESULTS

GlioSeq correctly identified 71/71 (100%) genetic alterations known to be present by conventional techniques, including 56 SNVs/indels, 9 CNVs, 3 EGFRvIII, and 3 KIAA1549-BRAF fusions. Only 20 ng of DNA and 10 ng of RNA were required for successful sequencing of 100% frozen and 96% formalin-fixed, paraffin-embedded tissue specimens. The assay sensitivity was 3%-5% of mutant alleles for SNVs and 1%-5% for gene fusions. The most commonly detected alterations were IDH1, TP53, TERT, ATRX. CDKN2A, and PTEN in high-grade gliomas, followed by BRAF fusions in low-grade gliomas and H3F3A mutations in pediatric gliomas.

CONCLUSIONS

GlioSeq NGS assay offers accurate and sensitive detection of a wide range of genetic alterations in a single workflow. It allows rapid and cost-effective profiling of brain tumor specimens and thus provides valuable information for patient management.

The Sensitive Detection of Telomerase Reverse Transcriptase Promoter Mutation by Amplification Refractory Mutation System-PCR

AIM

In gliomas, mutations in the core promoter region of the telomerase reverse transcriptase (TERT) gene have been associated with specific subtypes and are inversely correlated with IDH1 mutation status, predicting poor prognosis. Thus, TERT promoter mutation status might be a candidate for development as a prognostic biomarker. However, current IDH1 mutation detection methods using conventional polymerase chain reaction (PCR), followed by Sanger sequencing, have low sensitivity and are time-consuming. To improve test efficacy, we developed a more efficient detection protocol based on an amplification refractory mutation system-PCR (ARMS-PCR), which is based on the principle that DNA extension only happens when the 3'-terminal nucleotide of a primer matches its target sequence.

MATERIALS AND METHODS

We generated plasmids containing TERT promoter sequences and optimized this new protocol for the identification of the two most common TERT promoter mutations, C250T and C228T.

RESULTS

The enhanced sensitivity and efficiency of this protocol were validated using 124 human glioma samples.

CONCLUSION

We have described an ARMS-PCR methodology with improved sensitivities that could replace current commonly used methods for the detection of TERT promoter mutations in gliomas.

Molecular Pathways: Mitochondrial Reprogramming in Tumor Progression and Therapy

Small-molecule inhibitors of the phosphoinositide 3-kinase (PI3K), Akt, and mTOR pathway currently in the clinic produce a paradoxical reactivation of the pathway they are intended to suppress. Furthermore, fresh experimental evidence with PI3K antagonists in melanoma, glioblastoma, and prostate cancer shows that mitochondrial metabolism drives an elaborate process of tumor adaptation culminating with drug resistance and metastatic competency. This is centered on reprogramming of mitochondrial functions to promote improved cell survival and to fuel the machinery of cell motility and invasion. Key players in these responses are molecular chaperones of the Hsp90 family compartmentalized in mitochondria, which suppress apoptosis via phosphorylation of the pore component, Cyclophilin D, and enable the subcellular repositioning of active mitochondria to membrane protrusions implicated in cell motility. An inhibitor of mitochondrial Hsp90s in preclinical development (gamitrinib) prevents adaptive mitochondrial reprogramming and shows potent antitumor activity in vitro and in vivo. Other therapeutic strategies to target mitochondria for cancer therapy include small-molecule inhibitors of mutant isocitrate dehydrogenase (IDH) IDH1 (AG-120) and IDH2 (AG-221), which opened new therapeutic prospects for patients with high-risk acute myelogenous leukemia (AML). A second approach of mitochondrial therapeutics focuses on agents that elevate toxic ROS levels from a leaky electron transport chain; nevertheless, the clinical experience with these compounds, including a quinone derivative, ARQ 501, and a copper chelator, elesclomol (STA-4783) is limited. In light of this evidence, we discuss how best to target a resurgence of mitochondrial bioenergetics for cancer therapy.

PCR-Based Simple Subgrouping Is Validated for Classification of Gliomas and Defines Negative Prognostic Copy Number Aberrations in IDH Mutant Gliomas

Genetic subgrouping of gliomas has been emphasized recently, particularly after the finding of isocitrate dehydrogenase 1 (IDH1) mutations. In a previous study, we investigated whole-chromosome copy number aberrations (CNAs) of gliomas and have described genetic subgrouping based on CNAs and IDH1 mutations. Subsequently, we classified gliomas using simple polymerase chain reaction (PCR)-based methods to improve the availability of genetic subgrouping. We selected IDH1/2 and TP53 as markers and analyzed 237 adult supratentorial gliomas using Sanger sequencing. Using these markers, we classified gliomas into three subgroups that were strongly associated with patient prognoses. These included IDH mutant gliomas without TP53 mutations, IDH mutant gliomas with TP53 mutations, and IDH wild-type gliomas. IDH mutant gliomas without TP53 mutations, which mostly corresponded to gliomas carrying 1p19q co-deletions, showed lower recurrence rates than the other 2 groups. In the other high-recurrence groups, the median progression-free survival (PFS) and overall survival (OS) of patients with IDH mutant gliomas with TP53 mutations were significantly longer than those of patients with IDH wild-type gliomas. Notably, most IDH mutant gliomas with TP53 mutations had at least one of the CNAs +7q, +8q, −9p, and −11p. Moreover, IDH mutant gliomas with at least one of these CNAs had a significantly worse prognosis than did other IDH mutant gliomas. PCR-based mutation analyses of IDH and TP53 were sufficient for simple genetic diagnosis of glioma that were strongly associated with prognosis of patients and enabled us to detect negative CNAs in IDH mutant gliomas.

Insights into the clinical value of cyclin-dependent kinase 5 in glioma: a retrospective study

Background

Previous studies suggested that expression of cyclin-dependent kinase 5 (CDK5) may promote the migration and invasion of human glioma cells. In this study, we aimed to evaluate the clinical value of CDK5 in different grades of glioma in relation to Ki-67 labeling index (LI).

Methods

We firstly assessed by immunohistochemistry the expression of CDK5 in 152 glioma tissues and 16 normal brain tissues and further explored the relationship between CDK5 expression and other clinical features.

Results

The positive ratio of CDK5 in gliomas (57.2 %) was higher than that in normal brain tissues (12.5 %, P = 0.001). Difference of CDK5 expression among four World Health Organization (WHO) grades was statistically significant (P = 0.001). The significant differences of CDK5 expression were also observed between WHO I glioma (34.8 %) and WHO III glioma (62.5 %), as well as WHO IV glioma (82.8 %; P = 0.026, P < 0.001, respectively). Furthermore, Spearman’s rank correlation confirmed that CDK5 was positively correlated with the pathological grade of glioma (r = 0.831, P < 0.001). The CDK5 expression was also positively correlated with Ki-67 LI (r = 0.347, P < 0.001).

Conclusions

The current result suggests that CDK5 may play an essential role in the tumorigenesis and aggressiveness of gliomas.

Facing the future of brain tumor clinical research

This edition of CCR Focus provides critical reviews of several important areas in the field, including the application of findings from genomic investigations of brain tumors to improve diagnosis, clinical trial design, and ultimately optimizing individual patient treatment. Another article is a critical review provided by experts in the field that discusses the recent clinical trials using angiogenesis inhibitors, possible explanations for the results, and how to move forward. There is a concise discussion of the application of immunotherapy to brain tumors by key investigators in this field, reflecting the potential opportunities as well as the disease-specific challenges. Finally, leading pediatric brain tumor investigators provide an overview of the field and insights about the recent seminal discoveries in two pediatric brain tumors, supporting the paradigm that laboratory investigations lead to more precise diagnosis, prognosis, and ultimately better treatment. Herein, an overview of the recent advances and challenges in the area of clinical and translational brain tumor research is provided to set the stage for the contributions that follow.

Molecular insights into pediatric brain tumors have the potential to transform therapy

High-throughput genomic technologies have shed light on the biologic heterogeneity of several pediatric brain tumors. The biology of the four common pediatric brain tumors-namely medulloblastoma; ependymoma; high-grade glioma (HGG), including diffuse intrinsic pontine glioma; and low-grade glioma-is highlighted in this CCR Focus article. The discovery that medulloblastoma consists of four different subgroups, namely WNT, SHH, Group 3, and Group 4, each with distinct clinical and molecular features, has affected the treatment of children with medulloblastoma. Prospective studies have documented the efficacy of SMO inhibitors in a subgroup of patients with SHH medulloblastoma. Efforts are ongoing to develop specific therapies for each of the subgroups of medulloblastoma. Similar efforts are being pursued for ependymoma, HGG, and diffuse intrinsic pontine glioma where the disease outcome for the latter two tumors has not changed over the past three decades despite several prospective clinical trials. Developing and testing targeted therapies based on this new understanding remains a major challenge to the pediatric neuro-oncology community. The focus of this review is to summarize the rapidly evolving understanding of the common pediatric brain tumors based on genome-wide analysis. These novel insights will add impetus to translating these laboratory-based discoveries to newer therapies for children diagnosed with these tumors.

Do relevant markers of cancer stem cells CD133 and Nestin indicate a poor prognosis in glioma patients? A systematic review and meta-analysis

Background

CD133 and Nestin, as the markers of cancer stem cells, have recently been reported frequently in the pathogenesis and development of human gliomas. However, the prognostic role of CD133 and Nestin in gliomas still remains controversial. In this study, we aimed to evaluate the association between the expression of CD133 and Nestin and the outcome of glioma patients by conducting a systematic review and meta-analysis.

Methods

We performed systematically electronic and manual searches through the database of Pubmed and embase (until to December 25, 2014) for titles and abstracts which investigated the relationships between CD133 and Nestin expression and outcome of glioma patients. A systematic review and meta-analysis was executed to generate Pooled hazard ratios (HRs) with 95 % confidence intervals (CIs) for overall survival (OS) and progression-free survival (PFS).

Results

A total of 1,490 patients from 32 studies (13 articles) were included in the analysis. 19 studies and 13 studies investigated correlation between CD133 expression or Nestin and survival in gliomas, respectively. Our results showed that high CD133 expression in patients with glioma was associated with poor prognosis in terms of OS (HR 1.69; 95 % CI, 1.16–2.47; P =0.0060) and PFS (HR, 1.64; 95 % CI, 1.12–2.39; P = 0.010). In addition, high Nestin expression were associated with worse OS (HR 1.751; 95 % CI, 1.19–2.58, p = 0.004) but has no significant association with PFS (HR 1.55; 95 % CI, 0.96–2.51, p = 0.074). Even more important, the results of the subgroup meta-analyses show that that high CD133 expression was associated with worse prognosis in terms of OS and PFS in patients with WHO IV glioma but not WHO II-III. On the other hand, Nestin high expression was associated with worse prognosis in terms of OS and PFS in patients with WHO II-III glioma but not WHO IV.

Conclusion

High level of CD133 expression trends to correlate with a worse OS and PFS in glioma patients, especially WHO IV gliomas and Nestin high expression trends to correlate with a worse OS in glioma patients especially WHO II–III, revealing both the markers of cancer stem cells may as the potential pathological prognostic markers for glioma patients.

A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel

With the advent of large-scale genomic analysis, the genetic landscape of glioblastoma (GBM) has become more clear, including characteristic genetic alterations in EGFR. In routine clinical practice, genetic alterations in GBMs are identified using several disparate techniques that consume already limited amounts of tissue and add to overall testing costs. In this study, we sought to determine if the full spectrum of EGFR mutations in GBMs could be detected using a single next generation sequencing (NGS) based oncology assay in 34 consecutive cases. Using a battery of informatics tools to identify single nucleotide variants, insertions and deletions, and amplification (including variants EGFRvIII and EGFRvV), twenty-one of the 34 (62%) individuals had at least one alteration in EGFR by sequencing, consistent with published datasets. Mutations detected include several single nucleotide variants, amplification (confirmed by fluorescence in situ hybridization), and the variants EGFRvIII and EGFRvV (confirmed by multiplex ligation-dependent probe amplification). Here we show that a single NGS assay can identify the full spectrum of relevant EGFR mutations. Overall, sequencing based diagnostics have the potential to maximize the amount of genetic information obtained from GBMs and simultaneously reduce the total time, required specimen material, and costs associated with current multimodality studies.

Protein residues that control the reaction trajectory in S-adenosylmethionine radical enzymes: mutagenesis of asparagine 153 and aspartate 155 in Escherichia coli biotin synthase

Biotin synthase catalyzes the oxidative addition of a sulfur atom to dethiobiotin (DTB) to generate the biotin thiophane ring. This reaction is initiated by the reductive cleavage of the sulfonium center of S-adenosyl-L-methionine (AdoMet), generating methionine and a transient 5'-deoxyadenosyl radical that functions as an oxidant by abstracting hydrogen atoms from DTB. Biotin synthase contains a highly conserved sequence motif, YNHNLD, in which Asn153 and Asp155 form hydrogen bonds with the ribose hydroxyl groups of AdoMet. In the present work, we constructed four individual site-directed mutations to change each of these two residues in order to probe their role in the active site. We used molecular weight filtration assays to show that for most of the mutant enzymes binding of the substrates was only slightly affected. In vitro assays demonstrate that several of the mutant enzymes were able to reductively cleave AdoMet, but none were able to produce a significant amount of biotin. Several of the mutants, especially Asn153Ser, were able to produce high levels of the stable intermediate 9-mercaptodethiobiotin. Some of the mutants, such as Asp155Asn and Asn153Ala, produced instead an alternate product tentatively identified by mass spectrometry as 5'-mercapto-5'-deoxyadenosine, generated by direct attack of the 5'-deoxyadenosyl radical on the [4Fe-4S](2+) cluster. Collectively, these results suggest that the protein residues that form hydrogen bonds to AdoMet and DTB are important for retaining intermediates during the catalytic cycle and for targeting the reactivity of the 5'-deoxyadenosyl radical.